Molecular phylogeny of short-tailed opossums (Didelphidae: Monodelphis ): Taxonomic implications and tests of evolutionary hypotheses

Genetic and genomic architecture in eight strains of the laboratory opossum Monodelphis domestica

The gray short-tailed opossum (Monodelphis domestica) is an established laboratory-bred marsupial model for biomedical research. It is a critical species for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs ancestral states of genomic/epigenomic characteristics for eutherian mammal lineages. To characterize the current genetic profile of this laboratory marsupial, we examined 79 individuals from eight established laboratory strains. Double digest restriction site-associated DNA sequencing and whole-genome resequencing experiments were performed to investigate the genetic architecture in these strains. A total of 66,640 high-quality single nucleotide polymorphisms (SNPs) were identified. We analyzed SNP density, average heterozygosity, nucleotide diversity, and population differentiation parameter Fst within and between the eight strains. Principal component and population structure analysis clearly resolve the strains at the level of their ancestral founder populations, and the genetic architecture of these strains correctly reflects their breeding history. We confirmed the successful establishment of the first inbred laboratory opossum strain LSD (inbreeding coefficient F > 0.99) and a nearly inbred strain FD2M1 (0.98 < F < 0.99), each derived from a different ancestral background. These strains are suitable for various experimental protocols requiring controlled genetic backgrounds and for intercrosses and backcrosses that can generate offspring with informative SNPs for studying a variety of genetic and epigenetic processes. Together with recent advances in reproductive manipulation and CRISPR/Cas9 techniques for Monodelphis domestica, the existence of distinctive inbred strains will enable genome editing on different genetic backgrounds, greatly expanding the utility of this marsupial model for biomedical research.

Molecular Phylogeny of Cryptonanus (Didelphidae: Thylamyini): Evidence for a recent and complex diversification in South American open biomes

Systematic revisions of South American marsupials have contributed to our knowledge about genus and species diversity in the last decades, including studies of the most recently described genus Cryptonanus (Didelphidae), currently comprising four recognized species. Herein we provide the first phylogeny for these mouse opossums based on comprehensive sampling, including representatives from all nominal taxa, encompassing most of the geographic distribution of the genus while also extending its known range. The taxonomic status of Cryptonanus species was explored by analyses of multiple mitochondrial and nuclear DNA markers to assess phylogenetic relationships and to provide divergence time estimates, species delimitations and biogeographical hypotheses. Cryptonanus monophyly remained highly supported despite the inclusion of abundant new data from more than a hundred specimens, comprising 10 independent evolutionary lineages. Species-complexes within valid nominal taxa reveal higher species richness in the genus. Based on divergence estimates from a dated phylogeny, we suggest that Cryptonanus diversified along the Quaternary, with speciation events occurring well into the Pleistocene. The best supported biogeographical hypothesis endorses speciation by vicariance and subset speciation across open formations in shaping the evolutionary history of this didelphid genus, strongly associated with dry tropical landscapes of South America.

Potential mammalian species for investigating the past connections between Amazonia and the Atlantic Forest

Much evidence suggests that Amazonia and the Atlantic Forest were connected through at least three dispersion routes in the past: the Eastern route, the central route, and the Western route. However, few studies have assessed the use of these routes based on multiple species. Here we present a compilation of mammal species that potentially have dispersed between the two forest regions and which may serve to investigate these connections. We evaluate the present-day geographic distributions of mammals occurring in both Amazonia and the Atlantic Forest and the likely connective routes between these forests. We classified the species per habitat occupancy (strict forest specialists, species that prefer forest habitat, or generalists) and compiled the genetic data available for each species. We found 127 mammalian species presently occurring in both Amazonia and the Atlantic Forest for which, substantial genetic data was available. Hence, highlighting their potential for phylogeographic studies investigating the past connections between the two forests. Differently from what was previously proposed, the present-day geographic distribution of mammal species found in both Amazonia and the Atlantic Forest points to more species in the eastern portion of the dry diagonal (and adjoining forested habitats). The Central route was associated with the second most species. Although it remains to be seen how this present-day geography reflects the paleo dispersal routes, our results show the potential of using mammal species to investigate and bring new insights about the past connections between Amazonia and the Atlantic Forest.

Resistance of South American opossums to vWF-binding venom C-type lectins

Opossums in the clade Didelphini are well known to be resistant to snake venom due to endogenous circulating inhibitors which target metalloproteinases and phospholipases. However, the mechanisms through which these opossums cope with a variety of other damaging venom proteins are unknown. A protein involved in blood clotting (von Willebrand Factor) has been found to have undergone rapid adaptive evolution in venom-resistant opossums. This protein is a known target for a subset of snake venom C-type lectins (CTLs), which bind it and then induce it to bind platelets, causing hemostatic disruption. Several amino acid changes in vWF unique to these opossums could explain their resistance; however, experimental evidence that these changes disrupt venom CTL binding was lacking. We used platelet aggregation assays to quantify resistance to a venom-induced platelet response in two species of venom-resistant opossums (Didelphis virginiana, Didelphis aurita), and one venom-sensitive opossum (Monodelphis domestica). We found that all three species have lost nearly all their aggregation response to the venom CTLs tested. Using washed platelet assays we showed that this loss of aggregation response is not due to inhibitors in the plasma, but rather to the failure of either vWF or platelets (or both) to respond to venom CTLs. These results demonstrate the potential adaptive function of a trait previously shown to be evolving under positive selection. Surprisingly, these findings also expand the list of potentially venom tolerant species to include Monodelphis domestica and suggest that an ecological relationship between opossums and vipers may be a broader driver of adaptive evolution across South American marsupials than previously thought.

A revision of the Monodelphis glirina group (Didelphidae: Marmosini), with a description of a new species from Roraima, Brazil

Short-tailed opossums of the nominotypical subgenus Monodelphis occur throughout most of the cis-Andean lowlands of tropical South America. Among its member species, a monophyletic group that includes M. glirina (Amazonian red-sided opossum), M. sanctaerosae (Santa Rosa short-tailed opossum), and an unnamed taxon, herein referred to as the Monodelphis glirina group, is the focus of this paper. I provide an emended diagnosis for species of the group, information about geographic variation in M. glirina (including M. maraxina [Marajó short-tailed opossum]), and a formal description for the unnamed taxon mentioned above. The new species, known from two savanna localities in northeastern Roraima, is geographically disjunct from its closer relatives, M. glirina and M. sanctaerosae, only known to occur south of the Amazon. The new species differs from other congeneric taxa by a set of morphological characters and by DNA sequences.

Cuícas-de-cauda-curta do subgênero nominotípico Monodelphis ocorrem na maior parte das planícies cis-Andinas da América do Sul tropical. Dentre as espécies membro, o grupo monofilético que inclui M. glirina, M. sanctarosae, e um táxon ainda não descrito, referido como grupo Monodelphis glirina, é o foco do presente estudo. Aqui são fornecidas diagnoses emendadas para as espécies do grupo, informações sobre variação geográfica em M. glirina (incluindo M. maraxina), e descrição formal para o novo táxon mencionado acima. A nova espécie, conhecida de duas localidades de savana no nordeste de Roraima, encontra-se geograficamente disjunta das espécies mais proximamente relacionadas, M. glirina e M. sanctaerosae, somente conhecidas para a porção sul da Amazônia. A nova espécie difere das demais espécies congenéricas por um conjunto de características morfológicas e por sequências de DNA.

Minimal genetic divergence among South American samples of the water opossum Chironectes minimus: evidence for transcontinental gene flow?

Cytochrome b sequences from South American specimens of the water opossum Chironectes minimus exhibit uncorrected pairwise differences of 0.6% or less among samples collected thousands of kilometers apart (in Guyana, Bolivia and southeastern Brazil). Despite published evidence of population divergence from recent analyses of craniodental morphology, our results suggest extensive gene flow or recent range expansion across the South American landscapes currently occupied by this seldom-collected species.

Comparative cytogenetics of some marsupial species (Didelphimorphia, Didelphidae) from the Amazon basin

We investigated the karyotype of 18 didelphid species captured at 13 localities in the Brazilian Amazon, after conventional staining, C-banding, Ag-NOR and fluorescent in situ hybridization (FISH) using the 18S rDNA probe. Variations were found in the X chromosome, heterochromatin distribution and the 18S rDNA sequence. The main variation observed was in the position of the centromere in the X chromosome of Caluromys philander Linnaeus, 1758 and Marmosa murina Linnaeus, 1758. For both species, the X chromosome showed a geographical segregation in the pattern of variation between eastern and western Brazil, with a possible contact area in the central Amazon. C-banding on the X chromosome revealed two patterns for the species of Marmosops Matschie, 1916, apparently without geographic or specific relationships. The nucleolus organizer region (NOR) of all species was confirmed with the 18S rDNA probe, except on the Y chromosome of Monodelphis touan Shaw, 1800. The distribution of this marker varied only in the genus Marmosa Gray, 1821 [M. murina Thomas, 1905 and M. demerarae Thomas, 1905]. Considering that simple NORs are seen as a plesiomorphic character, we conclude that the species Marmosa spp. and Didelphis marsupialis Linnaeus, 1758 evolved independently to the multiple condition. By increasing the sample, using chromosomal banding, and FISH, we verified that marsupials present intra- and interspecific chromosomal variations, which suggests the occurrence of frequent chromosomal rearrangements in the evolution of this group. This observation contrasts with the chromosomal conservatism expected for didelphids.

Ontogeny of myosin isoform expression and prehensile function in the tail of the gray short-tailed opossum (Monodelphis domestica)

Terrestrial opossums use their semiprehensile tail for grasping nesting materials as opposed to arboreal maneuvering. We relate the development of this adaptive behavior with ontogenetic changes in myosin heavy chain (MHC) isoform expression from 21 days to adulthood. Monodelphis domestica is expected to demonstrate a progressive ability to flex the distal tail up to age 7 mo, when it should exhibit routine nest construction. We hypothesize that juvenile stages (3-7 mo) will be characterized by retention of the neonatal isoform (MHC-Neo), along with predominant expression of fast MHC-2X and -2B, which will transition into greater MHC-1β and -2A isoform content as development progresses. This hypothesis was tested using Q-PCR to quantify and compare gene expression of each isoform with its protein content determined by gel electrophoresis and densitometry. These data were correlated with nesting activity in an age-matched sample of each age group studied. Shifts in regulation of MHC gene transcripts matched well with isoform expression. Notably, mRNA for MHC-Neo and -2B decrease, resulting in little-to-no isoform translation after age 7 mo, whereas mRNA for MHC-1β and -2A increase, and this corresponds with subtle increases in content for these isoforms into late adulthood. Despite the tail remaining intrinsically fast-contracting, a critical growth period for isoform transition is observed between 7 and 13 mo, correlating primarily with use of the tail during nesting activities. Functional transitions in MHC isoforms and fiber type properties may be associated with muscle "tuning" repetitive nest remodeling tasks requiring sustained contractions of the caudal flexors.NEW & NOTEWORTHY Little is understood about skeletal muscle development as it pertains to tail prehensility in mammals. This study uses an integrative approach of relating both MHC gene and protein expression with behavioral and morphometric changes to reveal a predominant fast MHC expression with subtle isoform transitions in caudal muscle across ontogeny. The functional shifts observed are most notably correlated with increased tail grasping for nesting activities.

Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved.

Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation

We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyse the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and that this strong genetic covariation influenced the rate of morphological diversification of the brevicaudata group, with between-species divergence occurring fastest when occurring along the genetic line of least resistance. Accounting for the geometric distribution of genetic variation also increased our ability to detect the selective regimen underlying species diversification, with several instances of selection only being detected when genetic covariances were taken into account. Therefore, this work directly links patterns of genetic covariation among traits to macroevolutionary patterns of morphological divergence. Our findings also suggest that the limited distribution of Monodelphis species in morphospace is the result of a complex interplay between the limited dimensionality of available genetic variation and strong stabilizing selection along two major axes of genetic variation.